Računalna analiza povezanosti mikrobioma rodnice s HPV statusom u općoj populaciji žena

master's thesis

• Title (english): Computational analysis of the correlation between vaginal microbiota and HPV status in the general female population
• Author: Lovro Grum
• Mentor: Kristian Vlahoviček (mentor)
• Committee member: Kristian Vlahoviček (predsjednik povjerenstva)
• Committee member: Damjan Franjević (član povjerenstva)
• Committee member: Inga Urlić (član povjerenstva)
• Committee member: Rosa Karlić (član povjerenstva)
• Granter: University of Zagreb; Faculty of Science; (Department of Biology); Zagreb
• Defense date and country: 2024-06-21, Croatia
• Scientific / art field, discipline and subdiscipline: NATURAL SCIENCES; Biology

Abstract

Iako zauzima oko 9% mikrobioma žena, mikrobiom rodnice važan je za zdravlje ženskog reproduktivnog sustava. Zdrav mikrobiom rodnice karakterizira visoka zastupljenost bakterijskog roda Lactobacillus koji, osim snižavanjem pH, rodnicu često štiti proizvodnjom vodikova peroksida (H2O2). Mikrobiom se može proučavati metodama uzgoja bakterija, ali je na taj način nemoguće zabilježiti cjelokupnu mikrobnu bioraznolikost, niti je jednostavno proučavati ulogu, funkciju i interakciju mikrobioma s ogranizmom domaćinom. Umjesto toga, zahvaljujući napretku visokoprotočnog sekvenciranja, koristi se metagenomika. Njome se mikrobiom može proučavati izravno, bez uzgoja pojedinih vrsta ili sojeva, čime se, uz pripadajuću bioinformatičku analizu, mikrobiom može bolje taksonomski opisati, a omogućava se i njegovo funkcijsko opisivanje, primjerice analizom učestalosti upotrebe kodona. Pomoću dobivenih izvornih očitanja visokoprotočnog sekvenciranja metagenoma 10 uzoraka prikupljenih tijekom dobrovoljnog davanja brisa rodnice u svrhu testiranja na HPV, odredio sam taksonomski sastav mikrobioma unutar kraljevstva bakterija na svim taksonomskim razinama. Na temelju tih rezultata uzorke sam grupirao, te sam odredio gene i metaboličke puteve kojima su pojedine skupine uzoraka obogaćene. U konačnici sam ustanovio da postoje statistički značajne razlike između pojedinih skupina uzoraka u skladu s dosadašnjom literaturom, ali nisam mogao odrediti koje taksonomske skupine ili koja funkcija mikrobioma je povezana s povećanom zarazom HPV-a.

Abstract (english)

Although it occupies only about 9% of female's microbiome, microbiome of the uterus is important for the health of the female reproductive system. A healthy uterine microbiome is characterised by high abundance of bacterial genus Lactobacillus. The genus is protecting uterus by lowering its pH and producing hydrogen peroxide. Microbiome can be studied by cultivation method, which is unable to cover much of a microbial diversity and it is not providing easy functional analysis. Metagenomic is an alternative method enabled by high-throughput sequencing. It can be used for a direct taxonomic characterization of a microbiome, without prior cultivation, and it facilitates functional analysis of codon bias, by applying proper bioinformatic tools. I determined taxonomic composition for kingdom of Bacteria for all taxonomic levels to group 10 samples taken from volunteers that gave the samples from uterus to test them for the presence of HPV infection. Additionally, I determined genes and metabolic pathways for which the samples were enriched. Finally, I found that certain metadata is statistically significantly different between the samples in accordiance with current literature, but I could not determine which taxonomic units or function of microbiom are in correlation with HPV infection.

• Keywords: metagenomika; učestalost upotrebe kodona; metabolički putevi
• Keywords (english): metagenomics; codon bias; metabolic pathways
• Language: croatian
• URN:NBN: urn:nbn:hr:217:130671
• Study programme: Title: Molecular Biology; Study programme type: university; Study level: graduate; Academic / professional title: magistar/magistra molekularne biologije (magistar/magistra molekularne biologije)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Embargoed access; Embargo expiration date: 2026-06-21
• Created on: 2024-07-02 12:01:39